def __init__(self, **kwargs):
"""Initialize building block"""
super(pnetcdf, self).__init__(**kwargs)
self.__baseurl = kwargs.get(
'baseurl', 'https://parallel-netcdf.github.io/Release')
self.__configure_opts = kwargs.pop('configure_opts',
['--enable-shared'])
self.__ospackages = kwargs.pop('ospackages',
['m4', 'make', 'tar', 'wget'])
self.__prefix = kwargs.pop('prefix', '/usr/local/pnetcdf')
self.__runtime_ospackages = [] # Filled in by __distro()
self.__toolchain = kwargs.pop(
'toolchain',
toolchain(CC='mpicc',
CXX='mpicxx',
F77='mpif77',
F90='mpif90',
FC='mpifort'))
self.__url = None # Filled in by __download()
self.__version = kwargs.get('version', '1.12.1')
# Set the Linux distribution specific parameters
self.__distro()
# Set the download specific parameters
self.__download()
# Set the environment variables
self.environment_variables['PATH'] = '{}:$PATH'.format(
posixpath.join(self.__prefix, 'bin'))
if not self.ldconfig:
self.environment_variables[
'LD_LIBRARY_PATH'] = '{}:$LD_LIBRARY_PATH'.format(
posixpath.join(self.__prefix, 'lib'))
# Setup build configuration
self.__bb = generic_autotools(
comment=False,
configure_opts=self.__configure_opts,
devel_environment=self.environment_variables,
# For some compilers, --enable-shared leads to the following error:
# GEN libpnetcdf.la
# /usr/bin/ld: .libs/libpnetcdf.lax/libf77.a/strerrnof.o: relocation R_X86_64_32 against `.data' can not be used when making a shared object; recompile with -fPIC
# .libs/libpnetcdf.lax/libf77.a/strerrnof.o: error adding symbols: Bad value
# Apply the workaround
postconfigure=[
'sed -i -e \'s#pic_flag=""#pic_flag=" -fpic -DPIC"#\' -e \'s#wl=""#wl="-Wl,"#\' libtool'
] if '--enable-shared' in self.__configure_opts else None,
prefix=self.__prefix,
runtime_environment=self.environment_variables,
toolchain=self.__toolchain,
url=self.__url,
**kwargs)
# Container instructions
self += comment('PnetCDF version {}'.format(self.__version))
self += packages(ospackages=self.__ospackages)
self += self.__bb
def test_ldconfig_and_environment(self):
"""ldconfig and environment"""
g = generic_autotools(
devel_environment={
'CPATH': '/usr/local/zeromq/include:$CPATH',
'PATH': '/usr/local/zeromq/bin:$PATH'
},
ldconfig=True,
preconfigure=['./autogen.sh'],
prefix='/usr/local/zeromq',
repository='https://github.com/zeromq/libzmq.git',
runtime_environment={'PATH': '/usr/local/zeromq/bin:$PATH'})
self.assertEqual(
str(g), r'''# https://github.com/zeromq/libzmq.git
RUN mkdir -p /var/tmp && cd /var/tmp && git clone --depth=1 https://github.com/zeromq/libzmq.git libzmq && cd - && \
cd /var/tmp/libzmq && \
./autogen.sh && \
cd /var/tmp/libzmq && ./configure --prefix=/usr/local/zeromq && \
make -j$(nproc) && \
make -j$(nproc) install && \
echo "/usr/local/zeromq/lib" >> /etc/ld.so.conf.d/hpccm.conf && ldconfig && \
rm -rf /var/tmp/libzmq
ENV CPATH=/usr/local/zeromq/include:$CPATH \
PATH=/usr/local/zeromq/bin:$PATH''')
r = g.runtime()
self.assertEqual(
r, r'''# https://github.com/zeromq/libzmq.git
COPY --from=0 /usr/local/zeromq /usr/local/zeromq
RUN echo "/usr/local/zeromq/lib" >> /etc/ld.so.conf.d/hpccm.conf && ldconfig
ENV PATH=/usr/local/zeromq/bin:$PATH''')
def test_runtime(self):
"""Runtime"""
g = generic_autotools(
directory='tcl8.6.9/unix',
prefix='/usr/local/tcl',
url='https://prdownloads.sourceforge.net/tcl/tcl8.6.9-src.tar.gz')
r = g.runtime()
self.assertEqual(r,
r'''# https://prdownloads.sourceforge.net/tcl/tcl8.6.9-src.tar.gz
COPY --from=0 /usr/local/tcl /usr/local/tcl''')
def __init__(self, **kwargs):
"""Initialize building block"""
super(mpich, self).__init__(**kwargs)
self.__baseurl = kwargs.pop('baseurl',
'https://www.mpich.org/static/downloads')
self.__check = kwargs.pop('check', False)
self.__configure_opts = kwargs.pop('configure_opts', [])
self.__ospackages = kwargs.pop('ospackages', [])
self.__prefix = kwargs.pop('prefix', '/usr/local/mpich')
self.__runtime_ospackages = [] # Filled in by __distro()
# Input toolchain, i.e., what to use when building
self.__toolchain = kwargs.pop('toolchain', toolchain())
self.__version = kwargs.pop('version', '3.3.2')
# Output toolchain
self.toolchain = toolchain(CC='mpicc', CXX='mpicxx', F77='mpif77',
F90='mpif90', FC='mpifort')
# Set the configuration options
self.__configure()
# Set the Linux distribution specific parameters
self.__distro()
# Set the environment variables
self.environment_variables['PATH'] = '{}:$PATH'.format(
posixpath.join(self.__prefix, 'bin'))
if not self.ldconfig:
self.environment_variables['LD_LIBRARY_PATH'] = '{}:$LD_LIBRARY_PATH'.format(posixpath.join(self.__prefix, 'lib'))
# Setup build configuration
self.__bb = generic_autotools(
annotations={'version': self.__version},
base_annotation=self.__class__.__name__,
check=self.__check,
comment=False,
configure_opts=self.__configure_opts,
devel_environment=self.environment_variables,
# Run test suite (must be after install)
postinstall=['cd /var/tmp/mpich-{}'.format(self.__version),
'RUNTESTS_SHOWPROGRESS=1 make testing'] if self.__check else None,
prefix=self.__prefix,
runtime_environment=self.environment_variables,
toolchain=self.__toolchain,
url='{0}/{1}/mpich-{1}.tar.gz'.format(self.__baseurl,
self.__version),
**kwargs)
# Container instructions
self += comment('MPICH version {}'.format(self.__version))
self += packages(ospackages=self.__ospackages)
self += self.__bb
def test_package(self):
"""local package"""
g = generic_autotools(package='packages/openmpi-4.0.1.tar.bz2',
prefix='/usr/local/openmpi')
self.assertEqual(
str(g), r'''# packages/openmpi-4.0.1.tar.bz2
COPY packages/openmpi-4.0.1.tar.bz2 /var/tmp/openmpi-4.0.1.tar.bz2
RUN mkdir -p /var/tmp && tar -x -f /var/tmp/openmpi-4.0.1.tar.bz2 -C /var/tmp -j && \
cd /var/tmp/openmpi-4.0.1 && ./configure --prefix=/usr/local/openmpi && \
make -j$(nproc) && \
make -j$(nproc) install && \
rm -rf /var/tmp/openmpi-4.0.1 /var/tmp/openmpi-4.0.1.tar.bz2''')
def __init__(self, **kwargs):
"""Initialize building block"""
super(hdf5, self).__init__(**kwargs)
self.__baseurl = kwargs.pop(
'baseurl', 'http://www.hdfgroup.org/ftp/HDF5/releases')
self.__check = kwargs.pop('check', False)
self.__configure_opts = kwargs.pop(
'configure_opts', ['--enable-cxx', '--enable-fortran'])
self.__ospackages = kwargs.pop('ospackages', [])
self.__prefix = kwargs.pop('prefix', '/usr/local/hdf5')
self.__runtime_ospackages = [] # Filled in by __distro()
self.__version = kwargs.pop('version', '1.10.6')
# Set the Linux distribution specific parameters
self.__distro()
# Set the download specific parameters
self.__download()
# Set the environment variables
self.environment_variables['CPATH'] = '{}:$CPATH'.format(
posixpath.join(self.__prefix, 'include'))
self.environment_variables['HDF5_DIR'] = self.__prefix
self.environment_variables['LIBRARY_PATH'] = '{}:$LIBRARY_PATH'.format(
posixpath.join(self.__prefix, 'lib'))
self.environment_variables['PATH'] = '{}:$PATH'.format(
posixpath.join(self.__prefix, 'bin'))
if not self.ldconfig:
self.environment_variables[
'LD_LIBRARY_PATH'] = '{}:$LD_LIBRARY_PATH'.format(
posixpath.join(self.__prefix, 'lib'))
# Setup build configuration
self.__bb = generic_autotools(
annotations={'version': self.__version},
base_annotation=self.__class__.__name__,
check=self.__check,
configure_opts=self.__configure_opts,
comment=False,
devel_environment=self.environment_variables,
prefix=self.__prefix,
runtime_environment=self.environment_variables,
url=self.__url,
**kwargs)
# Container instructions
self += comment('HDF5 version {}'.format(self.__version))
self += packages(ospackages=self.__ospackages)
self += self.__bb
def test_defaults_ubuntu(self):
"""Default generic_autotools building block"""
g = generic_autotools(
directory='tcl8.6.9/unix',
prefix='/usr/local/tcl',
url='https://prdownloads.sourceforge.net/tcl/tcl8.6.9-src.tar.gz')
self.assertEqual(str(g),
r'''# https://prdownloads.sourceforge.net/tcl/tcl8.6.9-src.tar.gz
RUN mkdir -p /var/tmp && wget -q -nc --no-check-certificate -P /var/tmp https://prdownloads.sourceforge.net/tcl/tcl8.6.9-src.tar.gz && \
mkdir -p /var/tmp && tar -x -f /var/tmp/tcl8.6.9-src.tar.gz -C /var/tmp -z && \
cd /var/tmp/tcl8.6.9/unix && ./configure --prefix=/usr/local/tcl && \
make -j$(nproc) && \
make -j$(nproc) install && \
rm -rf /var/tmp/tcl8.6.9/unix /var/tmp/tcl8.6.9-src.tar.gz''')
def test_repository(self):
"""test repository option"""
g = generic_autotools(preconfigure=['./autogen.sh'],
prefix='/usr/local/zeromq',
repository='https://github.com/zeromq/libzmq.git')
self.assertEqual(str(g),
r'''# https://github.com/zeromq/libzmq.git
RUN mkdir -p /var/tmp && cd /var/tmp && git clone --depth=1 https://github.com/zeromq/libzmq.git libzmq && cd - && \
cd /var/tmp/libzmq && \
./autogen.sh && \
cd /var/tmp/libzmq && ./configure --prefix=/usr/local/zeromq && \
make -j$(nproc) && \
make -j$(nproc) install && \
rm -rf /var/tmp/libzmq''')
def test_runtime_annotate(self):
"""Runtime"""
g = generic_autotools(
annotate=True,
base_annotation='tcl',
directory='tcl8.6.9/unix',
prefix='/usr/local/tcl',
url='https://prdownloads.sourceforge.net/tcl/tcl8.6.9-src.tar.gz')
r = g.runtime()
self.assertEqual(
r,
r'''# https://prdownloads.sourceforge.net/tcl/tcl8.6.9-src.tar.gz
COPY --from=0 /usr/local/tcl /usr/local/tcl
LABEL hpccm.tcl.configure='./configure --prefix=/usr/local/tcl' \
hpccm.tcl.url=https://prdownloads.sourceforge.net/tcl/tcl8.6.9-src.tar.gz'''
)
def test_configure_opts_check(self):
"""Configure options and check enabled"""
g = generic_autotools(
check=True,
configure_opts=['--disable-getpwuid',
'--enable-orterun-prefix-by-default'],
prefix='/usr/local/openmpi',
url='https://www.open-mpi.org/software/ompi/v4.0/downloads/openmpi-4.0.1.tar.bz2')
self.assertEqual(str(g),
r'''# https://www.open-mpi.org/software/ompi/v4.0/downloads/openmpi-4.0.1.tar.bz2
RUN mkdir -p /var/tmp && wget -q -nc --no-check-certificate -P /var/tmp https://www.open-mpi.org/software/ompi/v4.0/downloads/openmpi-4.0.1.tar.bz2 && \
mkdir -p /var/tmp && tar -x -f /var/tmp/openmpi-4.0.1.tar.bz2 -C /var/tmp -j && \
cd /var/tmp/openmpi-4.0.1 && ./configure --prefix=/usr/local/openmpi --disable-getpwuid --enable-orterun-prefix-by-default && \
make -j$(nproc) && \
make -j$(nproc) check && \
make -j$(nproc) install && \
rm -rf /var/tmp/openmpi-4.0.1 /var/tmp/openmpi-4.0.1.tar.bz2''')
def test_environment_and_toolchain(self):
"""environment and toolchain"""
tc = toolchain(CC='gcc', CXX='g++', FC='gfortran')
g = generic_autotools(
build_directory='/tmp/build',
directory='/var/tmp/tcl8.6.9/unix',
environment={'FOO': 'BAR'},
prefix='/usr/local/tcl',
toolchain=tc,
url='https://prdownloads.sourceforge.net/tcl/tcl8.6.9-src.tar.gz')
self.assertEqual(str(g),
r'''# https://prdownloads.sourceforge.net/tcl/tcl8.6.9-src.tar.gz
RUN mkdir -p /var/tmp && wget -q -nc --no-check-certificate -P /var/tmp https://prdownloads.sourceforge.net/tcl/tcl8.6.9-src.tar.gz && \
mkdir -p /var/tmp && tar -x -f /var/tmp/tcl8.6.9-src.tar.gz -C /var/tmp -z && \
mkdir -p /tmp/build && cd /tmp/build && FOO=BAR CC=gcc CXX=g++ FC=gfortran /var/tmp/tcl8.6.9/unix/configure --prefix=/usr/local/tcl && \
make -j$(nproc) && \
make -j$(nproc) install && \
rm -rf /var/tmp/tcl8.6.9/unix /var/tmp/tcl8.6.9-src.tar.gz /tmp/build''')
def __init__(self, **kwargs):
"""Initialize building block"""
super(xpmem, self).__init__(**kwargs)
# Parameters
self.__branch = kwargs.pop('branch', 'master')
self.__configure_opts = kwargs.pop('configure_opts',
['--disable-kernel-module'])
self.__ospackages = kwargs.pop('ospackages', [
'autoconf', 'automake', 'ca-certificates', 'file', 'git',
'libtool', 'make'
])
self.__prefix = kwargs.pop('prefix', '/usr/local/xpmem')
self.__repository = kwargs.pop('repository',
'https://gitlab.com/hjelmn/xpmem.git')
# Setup the environment variables
self.environment_variables['CPATH'] = '{}:$CPATH'.format(
posixpath.join(self.__prefix, 'include'))
self.environment_variables['LIBRARY_PATH'] = '{}:$LIBRARY_PATH'.format(
posixpath.join(self.__prefix, 'lib'))
if not self.ldconfig:
self.environment_variables[
'LD_LIBRARY_PATH'] = '{}:$LD_LIBRARY_PATH'.format(
posixpath.join(self.__prefix, 'lib'))
# Setup build configuration
self.__bb = generic_autotools(
base_annotation=self.__class__.__name__,
branch=self.__branch,
comment=False,
configure_opts=self.__configure_opts,
devel_environment=self.environment_variables,
preconfigure=['autoreconf --install'],
prefix=self.__prefix,
repository=self.__repository,
runtime_environment=self.environment_variables,
**kwargs)
# Container instructions
self += comment('XPMEM branch {}'.format(self.__branch))
self += packages(ospackages=self.__ospackages)
self += self.__bb
def __init__(self, **kwargs):
"""Initialize building block"""
super(pmix, self).__init__(**kwargs)
self.__baseurl = kwargs.pop(
'baseurl',
'https://github.com/openpmix/openpmix/releases/download')
self.__check = kwargs.pop('check', False)
self.__ospackages = kwargs.pop('ospackages', [])
self.__prefix = kwargs.pop('prefix', '/usr/local/pmix')
self.__runtime_ospackages = [] # Filled in by __distro()
self.__version = kwargs.pop('version', '3.1.4')
# Set the Linux distribution specific parameters
self.__distro()
# Set the environment variables
self.environment_variables['CPATH'] = '{}:$CPATH'.format(
posixpath.join(self.__prefix, 'include'))
self.environment_variables['PATH'] = '{}:$PATH'.format(
posixpath.join(self.__prefix, 'bin'))
if not self.ldconfig:
self.environment_variables[
'LD_LIBRARY_PATH'] = '{}:$LD_LIBRARY_PATH'.format(
posixpath.join(self.__prefix, 'lib'))
# Setup build configuration
self.__bb = generic_autotools(
annotations={'version': self.__version},
base_annotation=self.__class__.__name__,
check=self.__check,
comment=False,
devel_environment=self.environment_variables,
prefix=self.__prefix,
runtime_environment=self.environment_variables,
url='{0}/v{1}/pmix-{1}.tar.gz'.format(self.__baseurl,
self.__version),
**kwargs)
# Container instructions
self += comment('PMIX version {}'.format(self.__version))
self += packages(ospackages=self.__ospackages)
self += self.__bb
def __init__(self, **kwargs):
"""Initialize building block"""
super(fftw, self).__init__(**kwargs)
self.__baseurl = kwargs.pop('baseurl', 'ftp://ftp.fftw.org/pub/fftw')
self.__check = kwargs.pop('check', False)
self.__configure_opts = kwargs.pop('configure_opts', [])
self.__directory = kwargs.pop('directory', '')
self.__mpi = kwargs.pop('mpi', False)
self.__ospackages = kwargs.pop('ospackages', ['file', 'make', 'wget'])
self.__prefix = kwargs.pop('prefix', '/usr/local/fftw')
self.__version = kwargs.pop('version', '3.3.8')
# Set the configure options
self.__configure()
# Set the environment variables
if not self.ldconfig:
self.environment_variables[
'LD_LIBRARY_PATH'] = '{}:$LD_LIBRARY_PATH'.format(
posixpath.join(self.__prefix, 'lib'))
# Setup build configuration
self.__bb = generic_autotools(
annotations={'version': self.__version},
base_annotation=self.__class__.__name__,
check=self.__check,
configure_opts=self.__configure_opts,
comment=False,
devel_environment=self.environment_variables,
# PGI compiler needs a larger stack size
postconfigure=['ulimit -s unlimited'] if self.__check else None,
prefix=self.__prefix,
runtime_environment=self.environment_variables,
url='{0}/fftw-{1}.tar.gz'.format(self.__baseurl, self.__version),
**kwargs)
# Container instructions
self += comment('FFTW version {}'.format(self.__version))
self += packages(ospackages=self.__ospackages)
self += self.__bb
def test_pre_and_post(self):
"""Preconfigure and postinstall options"""
g = generic_autotools(
directory='tcl8.6.9/unix',
postinstall=['echo "post"'],
preconfigure=['echo "pre"'],
prefix='/usr/local/tcl',
url='https://prdownloads.sourceforge.net/tcl/tcl8.6.9-src.tar.gz')
self.assertEqual(str(g),
r'''# https://prdownloads.sourceforge.net/tcl/tcl8.6.9-src.tar.gz
RUN mkdir -p /var/tmp && wget -q -nc --no-check-certificate -P /var/tmp https://prdownloads.sourceforge.net/tcl/tcl8.6.9-src.tar.gz && \
mkdir -p /var/tmp && tar -x -f /var/tmp/tcl8.6.9-src.tar.gz -C /var/tmp -z && \
cd /var/tmp/tcl8.6.9/unix && \
echo "pre" && \
cd /var/tmp/tcl8.6.9/unix && ./configure --prefix=/usr/local/tcl && \
make -j$(nproc) && \
make -j$(nproc) install && \
cd /usr/local/tcl && \
echo "post" && \
rm -rf /var/tmp/tcl8.6.9/unix /var/tmp/tcl8.6.9-src.tar.gz''')
def __init__(self, **kwargs):
"""Initialize building block"""
super(slurm_pmi2, self).__init__(**kwargs)
self.__baseurl = kwargs.pop('baseurl',
'https://download.schedmd.com/slurm')
self.__environment = kwargs.pop('environment', False)
self.__ospackages = kwargs.pop(
'ospackages', ['bzip2', 'file', 'make', 'perl', 'tar', 'wget'])
self.__prefix = kwargs.pop('prefix', '/usr/local/slurm-pmi2')
self.__version = kwargs.pop('version', '20.02.5')
# Setup the environment variables
self.environment_variables['CPATH'] = '{}:$CPATH'.format(
posixpath.join(self.__prefix, 'include', 'slurm'))
if not self.ldconfig:
self.environment_variables[
'LD_LIBRARY_PATH'] = '{}:$LD_LIBRARY_PATH'.format(
posixpath.join(self.__prefix, 'lib'))
# Setup build configuration
self.__bb = generic_autotools(
annotations={'version': self.__version},
base_annotation=self.__class__.__name__,
comment=False,
devel_environment=self.environment_variables,
environment=self.__environment,
install=False,
make=False,
postconfigure=['make -C contribs/pmi2 install'],
prefix=self.__prefix,
runtime_environment=self.environment_variables,
url='{0}/slurm-{1}.tar.bz2'.format(self.__baseurl, self.__version),
**kwargs)
# Container instructions
self += comment('SLURM PMI2 version {}'.format(self.__version))
self += packages(ospackages=self.__ospackages)
self += self.__bb
def __init__(self, **kwargs):
"""Initialize building block"""
super(cgns, self).__init__(**kwargs)
self.__baseurl = kwargs.pop('baseurl', 'https://github.com/CGNS/CGNS/archive')
self.__check = kwargs.pop('check', False)
self.__configure_opts = kwargs.pop('configure_opts',
['--with-hdf5=/usr/local/hdf5',
'--with-zlib'])
self.__ospackages = kwargs.pop('ospackages', [])
self.__prefix = kwargs.pop('prefix', '/usr/local/cgns')
self.__toolchain = kwargs.pop('toolchain', toolchain())
self.__version = kwargs.pop('version', '4.1.2')
# Set the configuration options
self.__configure()
# Set the Linux distribution specific parameters
self.__distro()
# Setup build configuration
self.__bb = generic_autotools(
annotations={'version': self.__version},
base_annotation=self.__class__.__name__,
check=self.__check,
comment=False,
configure_opts=self.__configure_opts,
directory=posixpath.join('CGNS-{}'.format(self.__version), 'src'),
prefix=self.__prefix,
toolchain=self.__toolchain,
url='{0}/v{1}.tar.gz'.format(self.__baseurl, self.__version),
**kwargs)
# Container instructions
self += comment('CGNS version {}'.format(self.__version))
self += packages(ospackages=self.__ospackages)
self += self.__bb
def build(container_format='singularity',
openmpi_version='2.0.4',
gnu_version='10',
cfdem_prefix='/usr/local/cfdem',
cfdem_version='3.8.0',
liggghts_prefix='/usr/local/ligghts',
lpp_prefix='/usr/local/lpp',
image='ubuntu:20.04',
mlton_version='on-20210117-release',
gmp_version='6.2.1'):
config.set_container_format(container_format)
stage0 = Stage(name='stage0')
stage0 += baseimage(image=image, _bootstrap='docker')
stage0 += label(metadata={
'maintainer': 'Luhan Cheng',
'email': '*****@*****.**'
})
stage0 += shell(commands=[
'rm /usr/bin/sh', 'ln -s /usr/bin/bash /usr/bin/sh', '/usr/bin/bash'
])
stage0 += packages(apt=[
'locales', 'wget', 'software-properties-common', 'git',
'build-essential', 'flex', 'bison', 'cmake', 'zlib1g-dev', 'gnuplot',
'libreadline-dev', 'libncurses-dev', 'libxt-dev', 'libscotch-dev',
'libptscotch-dev', 'libvtk6-dev', 'python-numpy', 'python-dev',
'qt5-default', 'git-core', 'libboost-system-dev',
'libboost-thread-dev', 'libqt5x11extras5-dev', 'qttools5-dev', 'curl',
'libgl1-mesa-dev', 'libosmesa6-dev', 'libssh2-1', 'libtool'
])
compilers = gnu(version=gnu_version)
stage0 += compilers
openmpi_building_block = openmpi(version=openmpi_version,
toolchain=compilers.toolchain,
cuda=False)
stage0 += openmpi_building_block
stage0 += generic_autotools(
url=f'https://gmplib.org/download/gmp/gmp-{gmp_version}.tar.xz',
prefix='/usr/local/gmp',
directory=f'gmp-{gmp_version}/',
)
stage0 += environment(variables=from_library('/usr/local/gmp'))
stage0 += generic_build(repository='https://github.com/MLton/mlton.git',
branch=mlton_version,
build=['make -j'],
install=['make PREFIX=/usr/local/mlton'])
if cfdem_version == '3.8.0':
OF_release = '5.x'
OF_commitHashtag = '538044ac05c4672b37c7df607dca1116fa88df88'
else:
raise Exception(
'Check https://github.com/CFDEMproject/CFDEMcoupling-PUBLIC/blob/master/src/lagrangian/cfdemParticle/cfdTools/versionInfo.H'
)
stage0 += comment('Obtain CFDEM source')
stage0 += shell(commands=[
f'mkdir -p {cfdem_prefix} {liggghts_prefix} {lpp_prefix}',
f'git clone --branch {cfdem_version} https://github.com/CFDEMproject/CFDEMcoupling-PUBLIC.git {cfdem_prefix}',
f'git clone --branch {cfdem_version} https://github.com/CFDEMproject/LIGGGHTS-PUBLIC.git {liggghts_prefix}',
f'git clone https://github.com/CFDEMproject/LPP.git {lpp_prefix}'
])
stage0 += comment('Install OpenFoam')
openfoam_prefix = f'/usr/local/OpenFOAM-{OF_release}'
thirdparty_prefix = f'/usr/local/ThirdParty-{OF_release}'
stage0 += shell(commands=[
f'mkdir -p {openfoam_prefix} {thirdparty_prefix}',
f'git clone https://github.com/OpenFOAM/OpenFOAM-{OF_release}.git {openfoam_prefix} && cd {openfoam_prefix} && git checkout {OF_commitHashtag}',
f'git clone https://github.com/OpenFOAM/ThirdParty-{OF_release}.git {thirdparty_prefix}',
])
stage0 += shell(commands=[
f'echo "source {openfoam_prefix}/etc/bashrc" >> ~/.bashrc',
])
# DLIB_PATH = '/usr/lib/x86_64-linux-gnu'
# INCLUDE_PATH = '/usr/include'
stage0 += shell_with_log(commands=[
f'{thirdparty_prefix}/Allwmake -j', # this breaks with openmpi >= 3, error: static assertion failed: "MPI_Type_extent was removed in MPI-3.0. Use MPI_Type_get_extent instead."
# f'{thirdparty_prefix}/makeParaView -mpi -mesa -mesa-lib {DLIB_PATH}/libOSMesa.so -mesa-include {INCLUDE_PATH}/GL -verbose',
f'{thirdparty_prefix}/makeParaView -mpi'
'wmRefresh'
])
stage0 += shell(commands=[
f'{openfoam_prefix}/Allwmake -j',
])
# /usr/bin/g++ -fPIC -O3 -DNDEBUG -Wl,--no-undefined -lc -shared -Wl,-soname,libvtkCommonSystem-pv5.4.so.1 -o ../../../lib/libvtkCommonSystem-pv5.4.so.1 CMakeFiles/vtkCommonSystem.dir/vtkClientSocket.cxx.o CMakeFiles/vtkCommonSystem.dir/vtkDirectory.cxx.o CMakeFiles/vtkCommonSystem.dir/vtkServerSocket.cxx.o CMakeFiles/vtkCommonSystem.dir/vtkSocket.cxx.o CMakeFiles/vtkCommonSystem.dir/vtkSocketCollection.cxx.o CMakeFiles/vtkCommonSystem.dir/vtkThreadMessager.cxx.o CMakeFiles/vtkCommonSystem.dir/vtkTimerLog.cxx.o -Wl,-rpath,/usr/local/ThirdParty-5.x/build/linux64Gcc/ParaView-5.4.0/lib: ../../../lib/libvtkCommonCore-pv5.4.so.1 ../../../lib/libvtksys-pv5.4.so.1 -lpthread -ldl
return stage0
def __init__(self, **kwargs):
"""Initialize building block"""
super(openmpi, self).__init__(**kwargs)
self.__baseurl = kwargs.pop('baseurl',
'https://www.open-mpi.org/software/ompi')
self.__configure_opts = kwargs.pop('configure_opts',
['--disable-getpwuid',
'--enable-orterun-prefix-by-default'])
self.__cuda = kwargs.pop('cuda', True)
self.__default_repository = 'https://github.com/open-mpi/ompi.git'
self.__infiniband = kwargs.pop('infiniband', True)
self.__ospackages = kwargs.pop('ospackages', [])
self.__pmi = kwargs.pop('pmi', False)
self.__pmix = kwargs.pop('pmix', False)
self.__prefix = kwargs.pop('prefix', '/usr/local/openmpi')
self.__recursive = kwargs.pop('recursive', True)
self.__runtime_ospackages = [] # Filled in by __distro()
# Input toolchain, i.e., what to use when building
# Create a copy of the toolchain so that it can be modified
# without impacting the original
self.__toolchain = _copy(kwargs.pop('toolchain', toolchain()))
self.__version = kwargs.pop('version', '4.0.5')
self.__ucx = kwargs.pop('ucx', False)
# Output toolchain
self.toolchain = toolchain(CC='mpicc', CXX='mpicxx', F77='mpif77',
F90='mpif90', FC='mpifort')
# Set the configure options
self.__configure()
# Set the Linux distribution specific parameters
self.__distro()
# Set the download specific parameters
self.__download()
kwargs['repository'] = self.repository
kwargs['url'] = self.url
# Setup the environment variables
self.environment_variables['PATH'] = '{}:$PATH'.format(
posixpath.join(self.__prefix, 'bin'))
if not self.ldconfig:
self.environment_variables['LD_LIBRARY_PATH'] = '{}:$LD_LIBRARY_PATH'.format(posixpath.join(self.__prefix, 'lib'))
# Setup build configuration
self.__bb = generic_autotools(
annotations={'version': self.__version} if not self.repository else {},
base_annotation=self.__class__.__name__,
comment=False,
configure_opts=self.__configure_opts,
devel_environment=self.environment_variables,
preconfigure=['./autogen.pl'] if self.repository else None,
prefix=self.__prefix,
recursive=self.__recursive,
runtime_environment=self.environment_variables,
toolchain=self.__toolchain,
**kwargs)
# Container instructions
if self.repository:
if self.branch:
self += comment('OpenMPI {} {}'.format(self.repository,
self.branch))
elif self.commit:
self += comment('OpenMPI {} {}'.format(self.repository,
self.commit))
else:
self += comment('OpenMPI {}'.format(self.repository))
else:
self += comment('OpenMPI version {}'.format(self.__version))
self += packages(ospackages=self.__ospackages)
self += self.__bb
def test_both_branch_and_commit(self):
"""both branch and commit"""
with self.assertRaises(RuntimeError):
g = generic_autotools(branch='dev', commit='deadbeef',
repository='foo')
def __init__(self, **kwargs):
"""Initialize building block"""
super(netcdf, self).__init__(**kwargs)
self.__baseurl_c = 'https://github.com/Unidata/netcdf-c/archive'
self.__baseurl_cxx = 'https://github.com/Unidata/netcdf-cxx4/archive'
self.__baseurl_fortran = 'https://github.com/Unidata/netcdf-fortran/archive'
self.__check = kwargs.pop('check', False)
self.__cxx = kwargs.pop('cxx', True)
self.__fortran = kwargs.pop('fortran', True)
self.__ospackages = kwargs.pop('ospackages', [])
self.__prefix = kwargs.pop('prefix', '/usr/local/netcdf')
self.__runtime_ospackages = [] # Filled in by __distro()
self.__version = kwargs.pop('version', '4.7.3')
self.__version_cxx = kwargs.pop('version_cxx', '4.3.1')
self.__version_fortran = kwargs.pop('version_fortran', '4.5.2')
# Set the Linux distribution specific parameters
self.__distro()
# Set the download specific parameters
self.__download()
# Setup the environment variables
self.environment_variables['CPATH'] = '{}:$CPATH'.format(
posixpath.join(self.__prefix, 'include'))
self.environment_variables['LIBRARY_PATH'] = '{}:$LIBRARY_PATH'.format(
posixpath.join(self.__prefix, 'lib'))
self.environment_variables['PATH'] = '{}:$PATH'.format(
posixpath.join(self.__prefix, 'bin'))
if not self.ldconfig:
self.environment_variables['LD_LIBRARY_PATH'] = '{}:$LD_LIBRARY_PATH'.format(posixpath.join(self.__prefix, 'lib'))
# Setup build configuration
comments = ['NetCDF version {}'.format(self.__version)]
self.__bb = [generic_autotools(
check=self.__check,
comment=False,
devel_environment=self.environment_variables,
directory=self.__directory_c,
prefix=self.__prefix,
runtime_environment=self.environment_variables,
url=self.__url_c,
**kwargs)]
# Setup optional CXX build configuration
if self.__cxx:
comments.append('NetCDF C++ version {}'.format(self.__version_cxx))
self.__bb.append(generic_autotools(
check=self.__check,
comment=False,
directory='netcdf-cxx4-{}'.format(self.__version_cxx),
# Checks fail when using parallel make. Disable it.
parallel=1 if self.__check else '$(nproc)',
prefix=self.__prefix,
url='{0}/v{1}.tar.gz'.format(self.__baseurl_cxx,
self.__version_cxx),
**kwargs))
# Setup optional Fortran build configuration
if self.__fortran:
comments.append('NetCDF Fortran version {}'.format(self.__version_fortran))
self.__bb.append(generic_autotools(
check=self.__check,
comment=False,
directory='netcdf-fortran-{}'.format(self.__version_fortran),
# Checks fail when using parallel make. Disable it.
parallel=1 if self.__check else '$(nproc)',
prefix=self.__prefix,
url='{0}/v{1}.tar.gz'.format(self.__baseurl_fortran,
self.__version_fortran),
**kwargs))
# Container instructions
self += comment(', '.join(comments))
self += packages(ospackages=self.__ospackages)
self += [bb for bb in self.__bb]
def build(container_format='singularity',
os_release='ubuntu',
os_version='20.04'):
config.set_container_format(container_format)
image = f'{os_release}:{os_version}'
stage0 = Stage(name='stage0')
stage0 += baseimage(image=image, _bootstrap='docker')
stage0 += environment(variables={
'LC_ALL': 'en_AU.UTF-8',
'LANGUAGE': 'en_AU.UTF-8',
})
stage0 += label(metadata={
'maintainer': 'Luhan Cheng',
'email': '*****@*****.**'
})
stage0 += shell(commands=[
'rm /usr/bin/sh', 'ln -s /usr/bin/bash /usr/bin/sh', '/usr/bin/bash'
])
stage0 += packages(apt=[
'wget', 'git', 'software-properties-common', 'build-essential',
'locales', 'zlib1g-dev', 'perl', 'ncbi-blast+', 'libx11-dev'
])
stage0 += shell(commands=['locale-gen en_AU.UTF-8'])
stage0 += gnu(version='10')
stage0 += generic_build(
url=
'http://search.cpan.org/CPAN/authors/id/Y/YA/YANICK/Parallel-ForkManager-1.19.tar.gz',
prefix='/usr/local/parallel-forkmanager',
build=['perl Makefile.PL', 'make install'],
install=['mv * /usr/local/parallel-forkmanager/'])
stage0 += environment(
variables=add_binary('/usr/local/parallel-forkmanager'))
stage0 += generic_build(
url=
'ftp://ftp.ebi.ac.uk/pub/software/clustalw2/2.1/clustalw-2.1-linux-x86_64-libcppstatic.tar.gz',
prefix='/usr/local/clustalw',
install=['mv clustalw2 /usr/local/clustalw/clustalw'])
stage0 += environment(variables=add_binary('/usr/local/clustalw'))
stage0 += generic_autotools(
url='ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-6.6.0.tar.gz',
prefix='/usr/local/emboss',
)
stage0 += environment(variables=from_prefix('/usr/local/emboss'))
stage0 += generic_autotools(
url=
'https://www.tbi.univie.ac.at/RNA/download/sourcecode/2_4_x/ViennaRNA-2.4.17.tar.gz',
prefix='/usr/local/viennarna')
stage0 += environment(variables=from_prefix('/usr/local/viennarna'))
stage0 += generic_build(
url='https://github.com/weizhongli/cdhit/archive/V4.8.1.tar.gz',
prefix='/usr/local/cdhit',
directory='cdhit-4.8.1',
build=['make'],
install=['mv * /usr/local/cdhit/'])
stage0 += environment(variables=add_binary('/usr/local/cdhit'))
stage0 += generic_build(
repository='https://github.com/ambarishbiswas/CRISPRDetect_2.2.git',
commit='0f8249f',
prefix='/usr/local/crisprdetect',
install=['mv * /usr/local/crisprdetect/'])
stage0 += environment(variables=add_binary('/usr/local/crisprdetect'))
return stage0
def test_invalid_package(self):
"""invalid package url"""
with self.assertRaises(RuntimeError):
g = generic_autotools(url='https://foo/bar.sh')
def test_both_repository_and_url(self):
"""both repository and url"""
with self.assertRaises(RuntimeError):
g = generic_autotools(repository='foo', url='bar')
def test_no_url(self):
"""missing url"""
with self.assertRaises(RuntimeError):
g = generic_autotools()
def __init__(self, **kwargs):
"""Initialize building block"""
super(mvapich2, self).__init__(**kwargs)
self.__baseurl = kwargs.pop(
'baseurl',
'http://mvapich.cse.ohio-state.edu/download/mvapich/mv2')
self.__configure_opts = kwargs.pop('configure_opts',
['--disable-mcast'])
self.__cuda = kwargs.pop('cuda', True)
self.__gpu_arch = kwargs.pop('gpu_arch', None)
self.__ospackages = kwargs.pop('ospackages', [])
self.__preconfigure = []
self.__prefix = kwargs.pop('prefix', '/usr/local/mvapich2')
self.__runtime_ospackages = [] # Filled in by __distro()
# Input toolchain, i.e., what to use when building
self.__toolchain = kwargs.pop('toolchain', toolchain())
self.__version = kwargs.pop('version', '2.3.3')
# MVAPICH2 does not accept F90
self.toolchain_control = {
'CC': True,
'CXX': True,
'F77': True,
'F90': False,
'FC': True
}
# Output toolchain
self.toolchain = toolchain(CC='mpicc',
CXX='mpicxx',
F77='mpif77',
F90='mpif90',
FC='mpifort')
# Set the configure options
self.__configure()
# Set the Linux distribution specific parameters
self.__distro()
# Setup the environment variables
# Set library path
self.environment_variables['PATH'] = '{}:$PATH'.format(
posixpath.join(self.__prefix, 'bin'))
self.runtime_environment_variables['PATH'] = '{}:$PATH'.format(
posixpath.join(self.__prefix, 'bin'))
if not self.ldconfig:
self.environment_variables[
'LD_LIBRARY_PATH'] = '{}:$LD_LIBRARY_PATH'.format(
posixpath.join(self.__prefix, 'lib'))
self.runtime_environment_variables[
'LD_LIBRARY_PATH'] = '{}:$LD_LIBRARY_PATH'.format(
posixpath.join(self.__prefix, 'lib'))
if self.__cuda:
# Workaround for using compiler wrappers in the build stage
self.environment_variables[
'PROFILE_POSTLIB'] = '"-L{} -lnvidia-ml -lcuda"'.format(
'/usr/local/cuda/lib64/stubs')
# Setup build configuration
self.__bb = generic_autotools(
comment=False,
configure_opts=self.__configure_opts,
devel_environment=self.environment_variables,
preconfigure=self.__preconfigure,
prefix=self.__prefix,
runtime_environment=self.runtime_environment_variables,
toolchain=self.__toolchain,
url='{0}/mvapich2-{1}.tar.gz'.format(self.__baseurl,
self.__version),
**kwargs)
# Container instructions
self += comment('MVAPICH2 version {}'.format(self.__version))
self += packages(ospackages=self.__ospackages)
self += self.__bb
def __init__(self, **kwargs):
"""Initialize building block"""
super(hdf5, self).__init__(**kwargs)
self.__baseurl = kwargs.pop(
'baseurl', 'http://www.hdfgroup.org/ftp/HDF5/releases')
self.__check = kwargs.pop('check', False)
self.__configure_opts = kwargs.pop(
'configure_opts', ['--enable-cxx', '--enable-fortran'])
self.__ospackages = kwargs.pop('ospackages', [])
self.__prefix = kwargs.pop('prefix', '/usr/local/hdf5')
# Create a copy of the toolchain so that it can be modified
# without impacting the original
self.__toolchain = _copy(kwargs.pop('toolchain', toolchain()))
self.__runtime_ospackages = [] # Filled in by __distro()
self.__version = kwargs.pop('version', '1.12.0')
# Set the Linux distribution specific parameters
self.__distro()
# Set the download specific parameters
self.__download()
# Set the environment variables
self.environment_variables['CPATH'] = '{}:$CPATH'.format(
posixpath.join(self.__prefix, 'include'))
self.environment_variables['HDF5_DIR'] = self.__prefix
self.environment_variables['LIBRARY_PATH'] = '{}:$LIBRARY_PATH'.format(
posixpath.join(self.__prefix, 'lib'))
self.environment_variables['PATH'] = '{}:$PATH'.format(
posixpath.join(self.__prefix, 'bin'))
if not self.ldconfig:
self.environment_variables[
'LD_LIBRARY_PATH'] = '{}:$LD_LIBRARY_PATH'.format(
posixpath.join(self.__prefix, 'lib'))
# PIC workaround when using the NVIDIA compilers
if self.__toolchain.FC and re.match('.*nvfortran',
self.__toolchain.FC):
if not self.__toolchain.FCFLAGS:
self.__toolchain.FCFLAGS = '-fpic -DPIC'
# Setup build configuration
self.__bb = generic_autotools(
annotations={'version': self.__version},
base_annotation=self.__class__.__name__,
check=self.__check,
configure_opts=self.__configure_opts,
comment=False,
devel_environment=self.environment_variables,
prefix=self.__prefix,
runtime_environment=self.environment_variables,
toolchain=self.__toolchain,
url=self.__url,
**kwargs)
# Container instructions
self += comment('HDF5 version {}'.format(self.__version))
self += packages(ospackages=self.__ospackages)
self += self.__bb
def __init__(self, **kwargs):
"""Initialize building block"""
super(ucx, self).__init__(**kwargs)
# Parameters
self.__baseurl = kwargs.pop(
'baseurl', 'https://github.com/openucx/ucx/releases/download')
self.__configure_opts = kwargs.pop('configure_opts', [
'--enable-optimizations', '--disable-logging', '--disable-debug',
'--disable-assertions', '--disable-params-check',
'--disable-doxygen-doc'
])
self.__cuda = kwargs.pop('cuda', True)
self.__default_repository = 'https://github.com/openucx/ucx.git'
self.__gdrcopy = kwargs.pop('gdrcopy', '')
self.__knem = kwargs.pop('knem', '')
self.__ofed = kwargs.pop('ofed', '')
self.__ospackages = kwargs.pop('ospackages', [])
self.__prefix = kwargs.pop('prefix', '/usr/local/ucx')
self.__runtime_ospackages = [] # Filled in by __distro()
self.__toolchain = kwargs.pop('toolchain', toolchain())
self.__version = kwargs.pop('version', '1.8.0')
self.__xpmem = kwargs.pop('xpmem', '')
# Set the configure options
self.__configure()
# Set the Linux distribution specific parameters
self.__distro()
# Set the download specific parameters
self.__download()
kwargs['repository'] = self.repository
kwargs['url'] = self.url
# Setup the environment variables
self.environment_variables['PATH'] = '{}:$PATH'.format(
posixpath.join(self.__prefix, 'bin'))
if not self.ldconfig:
self.environment_variables[
'LD_LIBRARY_PATH'] = '{}:$LD_LIBRARY_PATH'.format(
posixpath.join(self.__prefix, 'lib'))
# Setup build configuration
self.__bb = generic_autotools(
annotations={'version': self.__version}
if not self.repository else {},
base_annotation=self.__class__.__name__,
comment=False,
configure_opts=self.__configure_opts,
devel_environment=self.environment_variables,
preconfigure=['./autogen.sh'] if self.repository else None,
prefix=self.__prefix,
runtime_environment=self.environment_variables,
toolchain=self.__toolchain,
**kwargs)
# Container instructions
if self.repository:
if self.branch:
self += comment('UCX {} {}'.format(self.repository,
self.branch))
elif self.commit:
self += comment('UCX {} {}'.format(self.repository,
self.commit))
else:
self += comment('UCX {}'.format(self.repository))
else:
self += comment('UCX version {}'.format(self.__version))
self += packages(ospackages=self.__ospackages)
self += self.__bb